* Update community meeting info in README file (#1327)

* Update cron tests (#1333)

Co-authored-by: Dominik Stańczak <[email protected]>

* Bump actions/setup-python from 2.2.2 to 2.3.0 (#1332)

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Use @namurphy's clever idea  to handle chat

* Disregard bot rights

Co-authored-by: Nick Murphy <[email protected]>

* Prepare release v0.7.0 (#1336)

* Add page on writing a changelog entry to the developer docs (#1198)

* Begin changelog guide in developer docs

* More on changelog guide

* Update changelog guide

* Make spelling of "changelog" consistent

The follows the spelling used on Wikipedia, which is also the spelling
used more commonly.

* Add changelog entry

* Expand guide for creating changelog entries

* Add pre-release step about updating changelog entries

* Update changelog guide

* Add changelog_guide to contributor guide doc page

* Update changelog guide

* Fix a typo in doc guide

* Add anchor to release guide

* Fix Sphinx formatting

* Update changelog guide

* Add a pre-release step for updating changelog entries

* Add label to Changelog Guide

* Switch up between changelog docs

I still have a bit more to do to complete this change.

* Refine changelog guide

* Update index, etc. for changelog guide

* Change toctree for changelog

* Add a note about towncrier create --edit

* Add changelog guide to sidebar

* Fix sidebar file location

* Fix the fix that I just "fixed"

Fixing the sidebar reference to the changelog guide.

* Discuss parametrization with argument unpacking in testing guide (#1316)

* Discuss parametrization with argument unpacking in testing guide

* Continue updates to doc guide

* Update testing guide

* Minor changes

* Add a changelog entry

* Change subsection title

* Consistentify reST indentations

* Parametrize tests for ion_sound_speed. Closes #1304 (#1313)

Co-authored-by: seanjunheng2 <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Resolving Issue #844, fixing warnings (#1345)

Co-authored-by: tlee0818 <[email protected]>
Co-authored-by: Andrew Sheng <[email protected]>
Co-authored-by: Terrance Takho Lee <[email protected]>
Co-authored-by: mahimapannala <[email protected]>
Co-authored-by: itsraashi <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Dominik Stańczak <[email protected]>

* Drop scipy-dev tests for now (#1347)

* Faster interpolation on 'grid' objects (#1295)

Co-authored-by: Dominik Stańczak <[email protected]>

* Enable sphinx-hoverxref for documentation (#1353)

Co-authored-by: Dominik Stańczak <[email protected]>

* Fix linter errors (#1356)

* Try to fix linter errors in validators.py

* Try to fix linter errors in plasmablob.py

* Try to fix linter errors in grids.py

* Try to fix linter errors in fit_functions.py

* Try to fix linter errors in checks.py

* Update docstring one-liners

* Add docstring for func_err

* Update docstrings in fit_functions.py

* Move docstring from __init__ to class

* Return fit_functions.py to previous state

* Ignore flake8 rst error in fit_functions.py

* Fixing remaining warnings in issue #844 (#1346)

* Greeter bot for new contributors (#1095)

Co-authored-by: Nick Murphy <[email protected]>

* Create example notebook that lets users input plasma properties and get plasma parameters (#1229)

* [notebook-939]: Create interactive notebook for calc parameters

* Calculate Properties - interactive notebook base architecture

This commit creates provision to add/ remove calculation paramters on demand

* Add changelog entry

* [WIP] added more functions

* Added and classified input parameters and unit options

* Add convert to Hz widget

* Scratch update

* Separate code away from notebook

* Add clear everything button

* Clear output and rename notebook

* better evaluation display

* Script to launch app using voila

* Update properties with more formulary functions

* Clear output container nit

* Address Review Comments

Fix changelog entry, Clear output entries, Fix properties typo
Privatization of internal classes

* Make classes and functions private and use enums for colors

* Install calculator as a standalone cmdline tool

Cross platform tested with windows , when there are no sufficient elevation rights
one can install it with --user flag to ignore installation

* Move Calculator to utils instead of root

* Add favicon and dark mode

* Remove use of os.system - error thrown by dlint

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Use run to prevent orphan process

* Graceful exit with message

* Move Calculator logic to utils

* Add notebook to installation and sphinx docstring

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Add missing dependency

* Add ipywidgets to installation requirements

* Fix build failure because of eg

* Fix lint failures

* Address Review Comments

* Add back requirements to fix merge conflict

* Fix Documentation Build failure

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Use abstractmethod wrapper and add period to all descriptions

For consistency within the description section

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Fix documentation build because of heading line

* adjust coverage settings

* Address Review Commits

Cleanup private member doc

Co-authored-by: Rajagopalan Gangadharan <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Dominik Stańczak <[email protected]>

* Two stages of tests (#1350)

* Bump actions/setup-python from 2.3.0 to 2.3.1 (#1343)

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* BibTeXify references in `plasmapy.formulary` (#1299)

* BibTeXify dielectric references

* BibTeXify references from coupling_parameter

* Use hyperlink for Knudsen number

* Minor formatting edit

* Inline link for mobility

* Add Chen reference and drop Callen draft book reference

We don't have a permalink for the Callen draft book, unfortunately.
It'd be helpful to replace it with another reference later on.

* Minor bibliography edits

* Update references in collisions.py

* Finish putting references in bibtex file

* Bibtexify dielectric.py more

* Update/remove references in drifts.py

* Update reference in parameters.py

* Update references in braginskii.py

* Bibtexify references in quantum.py

* Remove trailing commas

* Put in a missing comma

* Add references to bibtex file

* Update references

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Add changelog entry

* Use the same sorting for keys in @article entries

* Fix citation key

* Change editions from, e.g., "1" to "1st"

* Quotes around titles to preserve capitalization

* Preserve capitalization

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Add reST substitutions and use them in narrative docs (#1158)

* Expand xrefs in docs for particles

* Use substitutions in functional particles docs

* Use substitutions in nuclear.rst

* Use substitutions for docstrings of Particle instances

* Use substitution for ParticleTracker

* Formatting changes for stability.rst

* Fix ReST link in Particle

* Change file location to literal text

* Add change log entry

* Fix typo

* And inf and nan to Sphinx replacements

* Move substitutions for particle functions to common_links

* Revert "And inf and nan to Sphinx replacements"

This reverts commit 70777149da4c6c82672a6ceda4785b3c47c7af19.

* Update reST formatting

* Update changelog entry

* Add reST substitutions for nan and inf

* Fix a link

* Change substitutions to use correct modeul

* Minor formatting change for line length

* Fix lingering incorrect namespace

* Discuss module docstrings and `__all__` in documentation guide (#1359)

* Discuss module docstrings and __all__

* Minor rewording

* Add changelog entry

* Discuss connection between __all__ and star imports

Co-authored-by: Dominik Stańczak <[email protected]>

* Add an interface function that creates physical particle objects (#1365)

* Continue working on particle factory & tests

* Move particle factory function to a new file

This is to avoid having to avoid circularity. particle_class.py
defines Particle, and particle_collections.py imports Particle to
define ParticleList. Prior to this commit, we had the factory function
in particle_class.py, where it imported ParticleList.

* Allow first two arguments of CustomParticle to be switched

* Finish CustomParticle having reversed argument order

* Update particle factory

* Remove edits to CustomParticle

These edits were moved to a different pull request.

* Add changelog entry

* Simplify discussion of parameters

* Mark a test as xfail

This will be ex-xfailed after #1364 is merged.

* Temporarily add particle factory stuff to __all__

* Make particle factory function private

* Refine docs & tests of particle factory

* Use extract method refactoring pattern on `Particle.__init__` (#1368)

* Extract some methods from start of Particle.__init__

* Extract special particle creation method

* Create empty method to initialize atoms

* Expand method to create atoms

* Minor updates to Particle initialization

* Minor updates to Particle initialization

* Add changelog entry

* Minor formatting fix

Co-authored-by: Dominik Stańczak <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Co-authored-by: Dominik Stańczak <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Create helper function to sort an iterable into a `dict` with `PhysicalType` objects as keys (#1360)

* Begin function to sort by physical type

* First draft of get_physical_type_dict

* First draft of get_physical_type_dict tests

* Add a changelog entry

* Make function private

* Make function private - part 2

* Add file docstring for tests

* Add test case and expand docstring

* Require Astropy v4.3.1 or newer

...for PhysicalType functionality.

* Update astropy version in tox.ini

* Mention Astropy version increase

* Describe more `make` environments for doc build in doc guide (#1373)

* Describe more make envs for doc build

* Adjust line length

* Add changelog entry

* Update copyright year in license to 2022

* Minor docstring fixes in `plasmapy.formulary` (#1376)

* Minor docstring edits to braginskii.py

* Minor docstring edits to mathematics.py

* Minor docstring edits to parameters.py

* Minor docstring edits to quantum.py

* Minor docstring edits to radiation.py

* Minor docstring edits to braginskii.py

* Minor docstring edits to mathematics.py

* Minor docstring edits to quantum.py

* Revert pygments style to `"default"` and set minimum version of pygments to 2.11.0 (#1361)

* Put references in bibliography (#1374)

* Minor docstring fixes in `thomson.py` and `langmuir.py` (#1375)

* Add `ParticleList.is_category` (#1378)

* Add tests for ParticleList.is_category

* Add ParticleList.is_category

* Add changelog entry

* Update changelog

* Minor edits to ParticleList.is_category docstring

* Fix coupling_parameter Docstring (#1379)

* Fix coupling_parameter Docstring

* Create 1379.doc

* Rename 1379.doc to 1379.doc.rst

* Update changelog/1379.doc.rst

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/formulary/collisions.py

Co-authored-by: Nick Murphy <[email protected]>

Co-authored-by: Nick Murphy <[email protected]>

* Lite-Functions Ep. 1 | Jump to Hyperspace (#1145)

@namurphy Thank you for the thorough review!

* Lite-Functions Ep. 2 | plasma_frequency_lite (#1308)

* Hollweg dispersion solver (#1189)

* Add Python 3.10 tests to GitHub Actions (#1292)

* Add Python 3.10 to tests

* Add changelog entry

* Special casing 3.10

due to https://github.com/actions/setup-python/issues/249#issuecomment-934299359

* Remove yaml pre-commit hook

due to "3.10" special case

* Update .pre-commit-config.yaml

* Update .pre-commit-config.yaml

* Update setup.cfg with Python 3.10

* Update long lines in README to trigger tests

* Switch Python 3.9 and 3.10 tests

* Fix typo in README.md

Co-authored-by: Dominik Stańczak <[email protected]>

* Describe plasma_calculator in narrative documentation (#1390)

* Add plasma calculator to docs

* Add changelog entry

* Trim header guards

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Address review comments

* Update docs/plasma_calculator/index.rst

* Update changelog/1390.doc.rst

* Update docs/plasma_calculator/index.rst

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Nick Murphy <[email protected]>

* Add a function to create CustomParticles from molecule symbols. (#1309)

* Added a molecule function to create CustomParticles From symbols.

* Typos and linter fix

* Changed error message if a molecule contains something that is not an element.

* Added changelog

* Made parsing stricter.

* Added tests

* Fixed tests

* Removed useless errors

* Apply suggestions from code review

Co-authored-by: Nick Murphy <[email protected]>

* Upgraded docstring to numpy style

* Finished docstring

* Parametrized tests

* Linters fix

* Missing indent

* RST203 fix

* Added examples

* Fixed doctest

* Apply suggestions from code review

Various typos

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/particles/particle_class.py

added Optional marker

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/particles/tests/test_particle_class.py

Added failing test before fixing.

Co-authored-by: Nick Murphy <[email protected]>

* Added error in case of a symbol containing an particle that is not an element
and a typo

* pre-commit applied

* Apply suggestions from code review

style upgrade

Co-authored-by: Nick Murphy <[email protected]>

Co-authored-by: Nick Murphy <[email protected]>

* Apply changes from static analysis tool that looks for likely bugs and design problems (#1282)

* Enable flake8-bugbear in tox linters

* Change lstrip to replace for multi-character string

This is from flake8-bugbear code B005.

* Remove unused variable in loop

* Remove redundant exceptions

* Remove redundant exceptions

* Remove redundant exceptions

* Set attribute directly instead of with setattr

* Use _ as an unused loop variable

* Simplify loop

* Update plasmapy/diagnostics/thomson.py

* Remove flake8-bugbear from testenv:linters

Co-authored-by: Dominik Stańczak <[email protected]>

* Changed CustomParticle __repr__ to display the symbol if present (#1397)

* Changed CustomParticle repr

* added changelog

* Update changelog/1397.breaking.rst

Co-authored-by: Nick Murphy <[email protected]>

Co-authored-by: Nick Murphy <[email protected]>

* Remove warnings from `CustomParticle` and `DimensionlessParticle` for `nan` attributes (#1399)

* [Docs] Refactor `version`, `release`, and `revision` definitions in `conf.py` (#1407)

* Update of pre-commit configuration and associated notebook autoformatting (#1408)

* Improve accessibility of documentation by increasing contrast for different website elements (#1287)

* Increase contrast of literal text

* Update colors of code snippets

* Make CSS selectors more specific

After reading some of the "Heck Yes! CSS!" zine by Julia Evans.

* Add a changelog entry

* Change CSS selector to match elements with multiple class names

...maybe this will work?

* Add comments to CSS file and change background

* Add CSS linter to pre-commit configuration

* Add more comments to CSS file

* Alphabetize some of the properties in CSS file

* Add a header to the CSS file

This header was motivated by it taking me a few hours to learn enough
CSS to understand this file. I suspect that most plasma physicists are
unfamiliar with CSS, so this header includes some information that would
have saved me maybe half of that time.  This includes...

 - A short overview of CSS rule syntax
 - Links to CSS resources
 - How to inspect an element in a web browser
 - Some best practices

* Update CSS rules for literals and hyperlinks

* Condense link CSS rules

* Adjustments to CSS styles

* Try to increase specificity of link color changes

...trying to avoid changes to the sidebar

* Re-add accidentally deleted notebook

* Change specificity of CSS selector

Trying to choose all of the stuff that is not in the sidebar

* Fix re-adding of accidentally deleted notebook

* Change specificity CSS selector

* Improve contrast for text in footers

This includes contrasts between the footer, the background, and links.

* Update CSS specifiers for literals

* Change colors for admonitions

This commit comes from the file:
sphinx_rtd_theme_ext_color_contrast/_static/sphinx_rtd_theme_ext_color_contrast.css
in the GitHub repository:
https://github.com/AaltoSciComp/sphinx_rtd_theme_ext_color_contrast

* Minor edits to comments in CSS file

* Delete commented out lines

Co-authored-by: Erik Everson <[email protected]>

* Create subdirectory /docs/_static/css/

* Spin off CSS file for admonition color contrast

* Run pre-commit on testing.yml

* Add changelog entry about csslint

* Modify changelog for CSS modifications

* Add changelog entry on re-organizing CSS files

* Update changelog entry on re-organizing CSS files

* Remove obsolete comment

* Remove what was probably a typo or autoformatting thing

...see Erik's suggest of removing `,l` from the CSS file in the PR.

* Make literals closer to PlasmaPy Red while still having enough contrast

* Make literals closer to PlasmaPy Red while still having enough contrast

* Mention in comment on transitory nature of l̶i̶f̶e̶ Sphinx customizations

* set plasmapy.css priority (600) so it's highest

* Update docs/_static/css/plasmapy.css

* Update docs/_static/css/plasmapy.css

Co-authored-by: Erik Everson <[email protected]>

* remove commented out code

* move styles into the RTD override section

* modify css comments

* update background and font colors for the file role

* split changelog entry

Co-authored-by: Erik Everson <[email protected]>

* Adjust scipy intersphinx mapping (#1419)

* Clean up tests in particles (#1369)

Co-authored-by: Nick Murphy <[email protected]>

* Limit CODEOWNERS to pinging plasmapy-reviewers group (#1351)

* Created a nullpoint finder file which finds the nullpoints of a vector space (#1383)

* Created a nullpoint finder file which finds the nullpoints of a vector space using a trilinear approximation.

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Added changelog entry for nullpoint.py

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Corrected the errors

* Corrected errors

* Added the test file

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Fixed float error

* More tests for code coverage

* Added the docstrings

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Added the documentiation

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Fixed docstring error

* Fixing docstring

* Fixing docstring errors

* Fixing docstring

* Fixing documentation

* Changed vector_space as discussed.

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Fixed error

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Added new test

* Fixed formatting

* Fixed errors

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Updated the docstring

* Fixed formatting

* Added citation for trilinear nullpoint finder

* Fixed citation

* Added citation to docstring

* Update docs/api_static/plasmapy.analysis.nullpoint.rst

Co-authored-by: Nick Murphy <[email protected]>

* Update changelog/1383.feature.rst

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/tests/test_nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/tests/test_nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/tests/test_nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/tests/test_nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/tests/test_nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/tests/test_nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Testing

* Testing 2

* Fixed code repition problems

* Added my name to the credits page

* Added suggestions

* Changed variable name

* made function names private

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update docs/ad/analysis/index.rst

Co-authored-by: Nick Murphy <[email protected]>

* Simplified condition check

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Nick Murphy <[email protected]>

* Add numba.(n)jit decorators to coverage exclude (#1418)

* Add pytest-xdist to test reqs (#1431)

* Update `gyroradius` FutureWarning and tests (#1430)

Awesome! Thank you for the quick review!

* Bump actions/setup-python from 2.3.1 to 2.3.2 (#1417)

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Create and populate `plasmapy.formulary.lengths` (#1434)

@namurphy Thanks for the quick review!

* Create and populate `plasmapy.formulary.frequencies` (#1439)

* Configure `sphinx-hoverxref` (#1437)

* Fix bug with proton equality while continuing `Particle.__init__` refactoring (#1366)

* Add failing test for proton equality bug

* Add failing test for Particle("H", Z=1, mass_numb=1)

* Add a hack to fix proton equality bug

* A hack to try to fix

This bug suggests that Particle.__init__ could use some friendly
refactoring.

* Add changelog entry

* More extract method pattern from Particle.__init__

* Create inputs dict in Particle

* Use Particle._inputs instead of arguments to methods

* More extract method

* Move method around

* Minor reorganizing

* More re-organizing

* Rename variable

* Use _inputs instead of arguments

* Finally proton equality bug

* Renaming and reorganization

* Simplify naming

* Simplify naming

* Use _inputs

* Minor changes

* Minor changes

* Minor changes

* Minor changes

* Minor changes

* Renaming variables and some minor reorganization

* Renaming variables and reorganization

* Slight change to test

* Slight change to test

* Slight changes to tests

* Add second changelog entry

* Update docstrings

* Remove Particle.__name__

* Remove unnecessary .keys() for dicts

* Remove unnecessary .keys() for dicts

* Change Particle._inputs to Particle.__inputs

* Rename dict containing data about special particles

* Remove delattr of Particle.__inputs

* Remove unnecessary .keys() for dicts

* Remove unnecessary use of .keys() in tests

* Remove unnecessary import

* Add docstring back for Particle.__init__

Adding this line back because it might be responsible for some
documentation test failures that started happening soon after.

* Add back Particle.__name__

* Remove docstring for Particle.__init__

* Revert Particle.__name__ line to pre-PR form

* Add comment about Particle.__name__

* Updates following code review

* Add comment about why protons are being treated specially

* Migrate dimensionless functionality from `plasmapy.formulary.parameters` to `dimensionless` (#1444)

* Privatize some `plasmapy.particles` modules (#1440)

* Make particles.parsing a private module

* Make particles.elements a private module

* Make particles.isotopes a private module

* Continue name changes

* Continue name changes

* Continue name changes

* Rename particles.isotopes

* Use namespace

* Continue renaming

* Continue renaming

* Import modules instead of their contents

* Import modules instead of their contents

* Add changelog entry

* Add changelog entries

* Remove api_static page for particles.elements

* Remove api_static page for particles.isotopes

* Remove api_static page for particles.parsing

* Remove api_static page for particles.special_particles

* Add a docstring to element_obj_hook

This was copied directly from isotope_obj_hook.

* Update changelog entry

* Use double back ticks

* Use empty __all__ in private particles modules

I have been getting some documentation build errors related to these
modules. I'm attempting to empty __all__ to see if this will prevent
these doc build errors.

* Update changelog entries

* Update breaking changelog entries

* Update imports

* Remove leading underscores

* update auto-pop of __all__ so modules are excluded

* Revert "Use empty __all__ in private particles modules"

This reverts commit 50e902d1f5f3ff103e8630951874fe640510c909.

* Remove import of particle_zoo

* Update names in docstrings

* Update changelog entry

* Add docstring for particle_zoo

* Update changelog entry

* Add docstring for PeriodicTable

Co-authored-by: Erik <[email protected]>

* Fix links in changelog entries (#1415)

* Patch for #1444 (#1446)

* Create and populate `plasmapy.formulary.speeds` (#1448)

* Create and populate `plasmapy.formulary.misc` (#1453)

Excellent! Thank you.

* Bump actions/checkout from 2.4.0 to 3 (#1461)

* Bump actions/setup-python from 2.3.2 to 3 (#1459)

* Make `Z` and `mass_numb` parameters for `Particle` keyword-only (#1456)

* Make Z and mass_numb keyword-only in Particle

* Add changelog entry

* Raise explicit error

* Update explicit error message

* Allow multiple positional args in Particle error tests

* Test when Particle is provided with >1 positional arg

...since Z and mass_numb should be keyword-only.

* Remove coverage: ignore comment

* Hide page with stability of subpackages (#1466)

* Rename stability matrix page with underscore

* Add :orphan: to stability matrix

* Remove stability matrix

* Add comment that stability page is out-of-date

* Add changelog entry

* Add changelog entry

* Remove misplaced changelog entry

* Update changelog

* Add an example notebook to introduce `astropy.units` (#1380)

* Start a units & particles notebook

* Minor changes to units/particles notebook

* Add changelog entry

* Add first draft of particles section to notebook

* Add first draft of units section of notebook

* Rename notebook

* Remove particles portion of notebook

* Update changelog entry

* Second draft of units notebook

* Update units notebook and add raises-exception tag

* Update links in notebook

* Update links

* Update units notebook

* Update units notebook

* Refine units notebook

* Refine units notebook

* Use Astropy logo for units notebook

This is available under the CC BY-SA license at:
https://github.com/astropy/astropy-logo/blob/main/LICENSE

* Minor updates to units notebook

* Minor updates to units notebook

* Update units notebook with headings and stuff

* Update units notebook

* Update units notebook

* Update units notebook

* Fix link

* Move units notebook to getting_started directory

* Create getting started page for docs

* Add getting started section to examples page

* Update changelog entries

* Update changelog entries

* Update name of subpackage

* Update relative locations of files

* Fix relative links

* Move vision statement to 'all the rest' section of docs

* Add an intro sentence for getting started page

* Update astropy logo location

* Update keyword parameter for gyrodradius

* Use minimal tracebacks in notebook & hide cell

* Change cell metadata to hide cell

* Remove :glob: from nbsphinx gallery

* Update units notebook

* Update changelog/1380.doc.1.rst

Co-authored-by: Erik Everson <[email protected]>

* Expand units in PlasmaPy section

* Mention factor of 2π

Co-authored-by: Erik Everson <[email protected]>

* Update discussion on unit systems & eV

* Fix link

Co-authored-by: Erik Everson <[email protected]>

* Patch for PR #1453 (`plasmapy.formulary.misc`) (#1471)

* Apply automated Sourcery refactorings to `plasmapy.plasma` (#1464)

* Apply changes from Sourcery to grids.py

* Apply changes from Sourcery to plasma3d.py

* Apply changes from Sourcery to plasmablob.py

* Apply changes from Sourcery to test_grids.py

* Add comment back in

* Add changelog entry

* Use actual value rather than recalculate it

Co-authored-by: Erik Everson <[email protected]>

* Rearrange conditional block

* Fix import of _grab_charge

* Add link to Sourcery

* Change list comprehension

Co-authored-by: Erik Everson <[email protected]>

* Fix parentheses

Co-authored-by: Erik Everson <[email protected]>

* Improving code coverage for null point finder by adding unit test for the case when vector values are entered by the user (#1427)

* Added test case for manual vector values.

* Added changelog entry

* Added test for multiple nullpoints

* Improved coverage

* Improved coverage

* Improved coverage

* Removed checking on surfaces, possibly unnecessary

* Splitted equality and testing atol

* Update plasmapy/analysis/tests/test_nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update changelog/1427.trivial.rst

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/tests/test_nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Added docstring for bound functions

Co-authored-by: Nick Murphy <[email protected]>

* Bump minimum required version of Python from 3.7 to 3.8 (#1465)

* Update minimum version of Python in docs/

* Update minimum version of Python in testing configurations

* Update minimum version of Python in main __init__.py

* Update minimum version of Python in codemeta.json

* Update minimum version of Python in setup.cfg

* Add changelog entry

I'm not sure if this should be a removal or breaking, but for now I'm
putting it as a removal.

* Ignore coverage for Python version check

* Raise an ImportError if Python version is too low

* Add second changelog

* Set Python version to 3.8 for conda env

* Try minimum NumPy version of 1.19.0

* Revert "Try minimum NumPy version of 1.19.0"

This reverts commit b7144a1c1df88fa4ca6867352869527816ff26aa.

* Unpin h5py minimal dependency in tox.ini

* Require h5py >= 3.0.0

* Update changelog entries

* Update changelog entry

Co-authored-by: Erik Everson <[email protected]>

* Unspecify which version of python in docs shebang line

Co-authored-by: Erik Everson <[email protected]>

* Update changelog entry

Co-authored-by: Erik Everson <[email protected]>

* Update min ver of Python in code guide

* Update changelog/1465.trivial.1.rst

Co-authored-by: Erik Everson <[email protected]>

Co-authored-by: Erik Everson <[email protected]>

* Apply automated Sourcery refactorings to `plasmapy.particles` (#1479)

* Apply Sourcery refactorings to _elements.py

* Apply Sourcery refactorings to _isotopes.py

* Apply Sourcery refactorings to _parsing.py

* Apply Sourcery refactorings to _special_particles.py

* Apply Sourcery refactorings to atomic.py

* Apply Sourcery refactorings to decorators.py

* Apply Sourcery refactorings to ionization_state.py

* Apply Sourcery refactorings to ionization_state_collection.py

* Apply Sourcery refactorings to nuclear.py

* Apply Sourcery refactorings to particle_class.py

* Apply Sourcery refactorings to particle_collections.py

* Apply Sourcery refactorings to serialization.py

* Apply Sourcery refactorings to test_decorators.py

* Apply Sourcery refactorings to test_ionization_collection.py

* Apply Sourcery refactorings to test_ionization_state.py

* Apply Sourcery refactorings to test_particle_class.py

* Apply Sourcery refactorings to test_particle_collections.py

* Add changelog entry

* Use intermediate variable names for conditional

* Use itertools for nested loop

* Fix Particle.__eq__

* Change tuple to list

Co-authored-by: Erik Everson <[email protected]>

* Add blank line

Co-authored-by: Erik Everson <[email protected]>

* Restructure exception

* Restructure dictionary comprehensions

* Remove unnecessary list comprehension

Co-authored-by: Erik Everson <[email protected]>

* Remove duplicate line

Co-authored-by: Erik Everson <[email protected]>

Co-authored-by: Erik Everson <[email protected]>

* Apply automated changes from pyupgrade (#1485)

* Update docstring for `molecule` (#1455)

* Update molecule docstring

* Add changelog entry

* Update return value in docstring

* Update docstring

* Fix reST formatting

* Update docstrings related to molecule

* Remove Notes section

* Edit exception description

* Remove redundancy in exception naming

* Use `int` instead of integer in parameters section

Co-authored-by: Erik Everson <[email protected]>

* Update plasmapy/particles/_parsing.py

Co-authored-by: Erik Everson <[email protected]>

* Update parameter description

* Fix exception names

Co-authored-by: Erik Everson <[email protected]>

Co-authored-by: Erik Everson <[email protected]>

* Apply automated Sourcery refactorings to `plasmapy.utils` (#1463)

* Apply Sourcery refactorings for widget_helpers.py

* Apply Sourcery refactorings to checks.py

* Apply Sourcery refactorings to code_repr.py

* Apply Sourcery refactorings to datatype_factory_base.py

* Apply Sourcery refactorings to pytest_helpers.py

* Apply Sourcery refactorings to roman.py

* Make minor fixes to pytest_helpers.py

* Add changelog entry

* Use intermediate variable

* Minor formatting changes

* Remove unused imports

* Minor edits to plasma calculator docstrings

* Replace comment

* Re-add comment & refactor line

Co-authored-by: Erik Everson <[email protected]>

* Add blank line

Co-authored-by: Erik Everson <[email protected]>

* Add link for Sourcery

* Update plasmapy/utils/decorators/checks.py

Co-authored-by: Erik Everson <[email protected]>

Co-authored-by: Erik Everson <[email protected]>

* Lite-Functions Ep. 3 | plasma dispersion functions (#1473)

* Use short type hints in documented signatures (#1488)

* Add workflow to label PR's based on size (#1467)

* Add workflow to label PR's based on size

* Add changelog entry

* Fix yaml syntax errors

* Use LF instead of CRLF

* Address review commits

* Pretty format yaml

* Use different action to generate PR size labels (#1492)

* Use different action to generate PR size labels

* Add changelog entry

* Fix pretty printing

* Set message_if_xl to empty string

Co-authored-by: Nick Murphy <[email protected]>

* Separating null_point_find into two functions for better user experience (#1477)

* Added test case for manual vector values.

* Added changelog entry

* Added test for multiple nullpoints

* Improved coverage

* Improved coverage

* Improved coverage

* Removed checking on surfaces, possibly unnecessary

* Splitted equality and testing atol

* Seperated null point find

* Added changelog entry

* Fixed doc error

* Edited changelog/doc

* Fixed docstring error

* Update changelog/1477.trivial.rst

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Added typing hint

Co-authored-by: Nick Murphy <[email protected]>

* Correct apparent bug in langmuir.py (#1487)

* Fix broken hyperlinks (#1484)

* Fix broken hyperlinks

* Update discussion of CSS files

* Fix link for directory with CSS files

* Fix more links

* Update links

* Use citation for NRL fomrulary

* Update a link

* Fix two misspellings of PlasmaPy

* Use `codespell` for spellchecking (#1493)

* Use codespell to fix spellings

* Minor spelling fixes

* Add changelog entry

* Unchange typo fix in pre-executed notebook

* Re-run notebook to fix doc error

* Remove accidentally committed file

* Two more spelling fixes

* Re-run notebook after typo fix

* Add codespell configuration

* Add tox config for codespell

* Revise codespell config for tox

* Revise codespell config in setup.cfg

* Lite-Functions Ep. 4 | permittivity_1D_Maxwellian (#1476)

* Apply automated Sourcery refactorings to `plasmapy.formulary` (#1480)

* Apply Sourcery refactorings in braginskii.py

* Apply Sourcery refactorings in collisions.py

* Apply Sourcery refactorings in dielectric.py

* Apply Sourcery refactorings in dimensionless.py

* Apply Sourcery refactorings in distribution.py

* Apply Sourcery refactorings in frequencies.py

* Apply Sourcery refactorings in ionization.py

* Apply Sourcery refactorings in lengths.py

* Apply Sourcery refactorings in magnetostatics.py

* Apply Sourcery refactorings in mathematics.py

* Apply Sourcery refactorings in misc.py

* Apply Sourcery refactorings in quantum.py

* Apply Sourcery refactorings in relativity.py

* Apply Sourcery refactorings in speeds.py

* Apply Sourcery refactorings in test_transport.py

* Re-add comment

* Add changelog entry

* Revert some Sourcery changes

* Revert some Sourcery changes

* Revert some Sourcery changes

* Revert some Sourcery changes

* Revert some Sourcery changes

* Remove unnecessary comment

* Revert some Sourcery changes

* Temporarily revert file

* Apply some Sourcery changes

* Apply some Sourcery changes

* Use `contextlib.suppress` to suppress exceptions instead of `try` & `except` (#1494)

* Refactor exception suppression in formulary.__init__

* Refactor exception suppression in particles._factory

* Refactor exception suppression in checks.py

* Refactor exception suppression in grids.py

* Refactor exception suppression in particle_collections.py

* Add changelog entry

* Update reST formatting in changelog entry

* Set maximum requirement for `click` (#1504)

* Comment about click requirement

* Fix pre-commit config

* Bump codecov/codecov-action from 2.1.0 to 3 (#1506)

* Stop using `check-merge-conflicts` pre-commit hook for `.rst` files (#1505)

* Drop check-merge-conflicts from pre-commit config

* Exclude .rst files from pre-commit hook

* Add pre-commit hook for `absolufy-imports` (#1499)

* Add absolufy-imports to pre-commit

* Change imports from relative to absolute

* Add changelog entry

* Exclude `plasmapy_sphinx` from this hook

* Add common link for pre-commit.ci

...which is for the CI aspect of pre-commit.  This differs from the
regular pre-commit website.

* Revert plasmapy_sphinx

* Update changelog entry

* Bump actions/stale from 4 to 5 (#1508)

Bumps [actions/stale](https://github.com/actions/stale) from 4 to 5.
- [Release notes](https://github.com/actions/stale/releases)
- [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/stale/compare/v4...v5)

---
updated-dependencies:
- dependency-name: actions/stale
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#1377)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/pre-commit/pre-commit-hooks: v3.4.0 → v4.1.0](https://github.com/pre-commit/pre-commit-hooks/compare/v3.4.0...v4.1.0)
- [github.com/psf/black: 21.12b0 → 22.3.0](https://github.com/psf/black/compare/21.12b0...22.3.0)
- [github.com/nbQA-dev/nbQA: 0.8.0 → 1.3.1](https://github.com/nbQA-dev/nbQA/compare/0.8.0...1.3.1)
- [github.com/macisamuele/language-formatters-pre-commit-hooks: v2.1.0 → v2.3.0](https://github.com/macisamuele/language-formatters-pre-commit-hooks/compare/v2.1.0...v2.3.0)

* Use older version of black

...since the newer version of black drops spaces around the `**` operator in simple cases.

* Fix version of black

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Nick Murphy <[email protected]>

* Delete dependabot.yml (#1510)

As per https://github.com/dependabot/dependabot-core/issues/2804 and https://github.com/numpy/numpy/issues/18977, I'm proposing that we remove dependabot which ends up producing mostly noise rather than actual utility :(

* Add `analysis` and `dispersion` to `plasmapy.__init__` (#1512)

* Import analysis & dispersion in `plasmapy.__init__`

* Import analysis & dispersion to `__all__`

* Add a changelog entry

* Update changelog/1512.bugfix.rst

Co-authored-by: Erik Everson <[email protected]>

* Remove extra period

Co-authored-by: Erik Everson <[email protected]>

* Allow `Particle("Li").ionize()`, assuming meant as neutral atom (#1514)

* Allow Particle(Li).ionize(), assuming meant as neutral atom

* Add changelog entry

* Adjust docstrings

* Update changelog/1514.feature.rst

Co-authored-by: Nick Murphy <[email protected]>

Co-authored-by: Nick Murphy <[email protected]>

* Specify allowed roles & directives in docstrings (#1519)

* Reduce number of warnings for nitpicky doc builds (#1509)

* Make reST fixes for no longer defined code objects

* Add bibliography entry

* Minor text changes

* Use xarray substitution

* Use xarray substitution

* Fix reST links in plasmapy.plasma

* Fix reST links in 0.6.0.rst

* Fix reST links for plasma subclasses

* Remove reST link

* Update names of fit functions attributes

* Update xarray link

* Update xarray link

* Create conf var for nitpicky doc build ignore

* Make default sphinx role more explicit

* Split long line

* Use nitpick_ignore_regex

* Add cautionary comment

* Fix reST errors in testing_guide.rst

* Remove extra lines

* Fix reST link

* Fix reST links

* Fix reST links in checks.py

* Fix reST links in converter.py

* Fix reST link in helper.py

* Fix reST links in validators.py

* Fix reST links in pytest_helpers.py

* Fix reST links in braginskii.py

* Fix reST links for ionization state functionality

* Fix reST links in distribution.py

* Fix reST links in speeds.py

* Fix reST links in plasmapy.particles

* Update nitpicky doc build ignore patterns

* Add changelog entries

* Minor formatting

* Add changelog entry

* Fix reST links in pytest_helpers.py

* Fix reST links in tests.helpers.exceptions

* Fix reST link in swept Langmuir helpers

* Fix reST links

* Use Unicode arrows

* Expand commends in docs/conf.py

* Unicode changes

* Fix reST links attr names in fit_functions.py

* Fix scipy link (hopefully)

* Add pattern to nitpicky ignore regex

* Fix reST links in charged_particle_radiography.py

* Fix reST links in floating_potential.py

* Sort out usage of contextlib in formulary.__init__

* Fix reST links in collisions.py

* Fix reST links in dimensionless.py

* Fix reST links in distribution.py

* Fix reST links in formulary

* Fix reST typo

* Fix reST links

* Fix reST link

* Fix reST

* Fix reST

* Fix reST link

* Update nitpicky ignore regex

* reST fixes

* More reST fixes in plasmapy.particles

* A reST fix in testing_guide.rst

* Use reST role for conf val

* Expand patterns to ignore for nitpicky regex

* reST fix for particletracker.py

* reST fixes

* reST fixes

* reST fixes

* reST fixes

* reST fixes

* reST fixes

* Expand nitpicky ignore regex

* reST fixes

* reST fixes

* Move OpenPMD link to common_links.rst

* Allow imports not at top of formulary.__init__

* reST fixes

* Reorganize nitpick_ignore_regex

* Fix typo in reST link

* Update comments in nitpick_ignore_regex

* Fix reST link

* Extend nitpick_ignore_regex for reST workarounds

* reST fixes in code_guide.rst

* Fix name of package in nitpick_ignore_regex

* Fix reST link

* Minor reST fixes

* reST formatting for filename

* Update flake8 ignore option

* Minor docstring & link updates

* Minor docstring & link updates

* Describe doctests in documentation guide (#1478)

* Add doctests to documentation guide

* Add changelog entry

* Fix link

* Reword doctest documentation

* Reword doctest documentation

* Reword doctest documentation

* Update requirements and installation instructions (#1482)

* Remove env variable lines for minimal tests

* Bump minimum requirements

* Bump requirements

* Bump requirements

* Alphabetize environment.yml file

* Sort dependencies

* Consistentify formatting

* Add changelog entry

* Update changelog entry

* Add linters to tests requirements

* Significantly update environment.yml file

My intention for this particular file is to provide every dependency
needed for development of PlasmaPy, including docs & tests.  An
alternative would be to include only the requirements needed for
PlasmaPy users, which would be more appropriate for launching notebooks
on (for example) binder.

* Unrename conda environment

* Make conda environment depend solely on requirements.txt

* Alphabetize

* Update changelog entries

* Add common links for mpmath & xarray

* Update changelog entry with common links

* Update changelog entries

* Add pre-commit to extras requirements

* Remove information on dependencies from docs

* Use nested inline literal for xarray in docs

* Use link for pydocstyle

* Add yet another changelog entry

* Fix typo

* Update changelog entry

* Consistentify & reorganize requirements

* Fix misplaced comment

* Update changelog entry

* Reword changelog entry

* Fix typo

* Update changelog/1482.doc.rst

Co-authored-by: Erik Everson <[email protected]>

* Minor updates to installation instructions

* Update changelog entry

Co-authored-by: Erik Everson <[email protected]>

* Update installation instructions

* Update requirements

* Update installation instructions

* Reorganize beginning of installation instructions

Co-authored-by: Erik Everson <[email protected]>

* Update installation instructions

* Update installation instructions

* Move admonition

* Update installation instructions

* Update installation instructions

* Update installation instructions

* Update changelog entries

* Update changelog entries

* Deprecate `pip install plasmapy[all]`

* Add nested inline literals for different packages

* Reword installation instructions

* Fix link

* Add codespell to extras requirements

* Update changelogs slightly

* Update installation instructions

* Update installation instructions for Anaconda Navigator

* Update minimal testing env

* Consistency of requirements that are in multiple files

* Update installation instructions

* Update installation instructions

* Minor changes to installation instructions

* Update numba link to read the docs

* Remove pygments from tests dependencies

* Alphabetize requirements

* Have install.txt require build.txt requirements

* Remove setuptools from setup.cfg install requirements

* Remove setuptools from install requirements

* Remove setuptools_scm from extras requirements

* Remove ipywidgets from docs requirements

* Use -r install.txt for tests, docs, & extras

...and add a comment

* Reorganize imports

* Update section on obtaining source code

* Update section on installing with pip

* Update section headings

* Update Anaconda Nav instructions & add minpython substitution

* Update admonitions

* reST formatting after a substitution

* Add a linkcheck allowed redirect for xarray

* Remove optional_deps.py

This is no longer needed since we do not have optional dependencies
anymore. If we do add them back in at some point, we should re-use this.

* Remove optional_deps api_static page

* Update changelog entries

* Fix import associated with lmfit

* Put back in lines that should not have been removed

* Be more explicit about which versions of python

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Use |minpython| substitution in index page

* Include link to releases page in repo

* Remove lingering merge conflict string

Co-authored-by: Erik Everson <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Minor fixes in `plasmapy.formulary` from PyCharm & Sourcery (#1524)

* Minor grammar/formatting changes in braginskii.py

* Minor grammar/formatting change in collisions.py

* Raise from previous exception in frequencies.py

* Minor grammatical changes in lengths.py

* Use divquals operator in magnetostatics.py

* Typo fix in magnetostatics.py

* Use divquals operator in mathematics.py

* Raise from previous exception in misc.py

* Raise from previous exception in quantum.py

* Make docstring consistent with function signature

* Undo using divquals operator

I don't quite understand why, but this led to some errors.

* Undo using divquals operator

* Undo using divquals operator

* Revise `README.md` (#1495)

* Change time zone for meetings in `README.md`

* Significantly rewrite `README.md`

* Fix link

* More updates to README.md

* More updates to README.md

* Remove obsolete style linters badge

This was pointing to a workflow that was last run ten months ago,
though I'm not sure why.

* Mention installation via Anaconda Navigator

* Update Python installation instructions

* Update README.md

* Change development status to beta 🎉

* Fix unrelated typo

* Fix typo

* Update README.md

* Test that ``plasmapy`` can be imported (#1501)

* Test that plasmapy can be imported

* Add changelog entry

* Remove test_import.py

* Add first draft of github action for PRs

* Add import PlasmaPy to fortnightly tests

* Add GitHub Action for codespell (#1530)

* Add GitHub Action for codespell

* Update codespell config with intentional typo

* Update testing config to allow echo

* Update commands_post message for codespell in tox.ini

* Update testing guide on codespell github action

* Update commands_pre for codespell tox env

* Update codespell tox action

* Add missing reST link

* Update commands_pre & commands_post for codespell tox env

* Add changelog entries

* Update contextual information in codespell tox env

* Remove link

* Add Sphinx extensions (#1532)

* Add sphinx-notfound-page

* Add sphinx-notfound-page & sphinx-issues

* Use :user: role from sphinx-issues in credits.rst

* Add sphinx_issues to extensions

* Formatting

* Use sphinx.ext.extlinks & define :orcid:

* Add section heading comment

* Alphabetize rst-roles

* Apply :orcid: role

* Update :user: links for GitHub

* Apply extlinks

* Add a comment about how to sign up for ORCID

* Define reST link workarounds for sphinx extensions

* Add changelog entries

* Update requirements in setup.cfg

* Update to raw string

* Update documentation guide

* Use :wikipedia: role

* Exclude Untitled* from doc builds

...because I have a habit of creating untitled Jupyter notebooks.

* Use :wikipedia: role

* Update exclude_patterns

* Update changelog entries

* Update CSS link

* Update CSS links

* Use in-line if construction

* Update link

* Update links

* Allow redirects for Wikipedia for make linkcheck

This is because it showed redirects where the only difference was
capitalization of the first letter.

* Remove broken link

* Make flake8-rst-docstrings accept :wikipedia:

* Make flake8-rst-docstrings accept :wikipedia:

* Remove tentatively added extension

* Faster distributions (#1531)

Co-authored-by: Dominik Stańczak <[email protected]>

* Base bibliography html anchors on citation key (#1527)

* Base bibliography html anchors on citation key

* Update permanent redirect

* Replace broad exception statements in `formulary`, `particles`, and `utils` (#1541)

* Use narrower exception statements (#1525)

* Replace broad exception statements

* Add changelog entry

* Fix styling issue

* Fix styling issue

* Hollweg Dispersion Solver Bug Fix (#1529)

* Update node version to 16.15.0. (#1543)

* Fix to Z dependence in `fundamental_collision_freq`.  (#1546)

* Create `ParticleListLike` typing construct and "particle-list-like" term (#1528)

* Create particle-list-like term and ParticleListLike

* Add changelog entry

* Update `plasmapy.particles._parsing.extract_charge()` to better handle white spaces (#1555)

* Update docs and the use of `kwargs` in `fit_functions.Linear.curve_fit` (#1518)

* Update reST link and use kwargs

* Add changelog entry

* fix links to Linear.curve_fit (i.e. it's in the analysis pkg)

Co-authored-by: Erik <[email protected]>

* Add `flake8-implicit-str-concat` and `flake8-mutable` extensions to linters (#1557)

* Add flake8-implicit-str-concat to linters

* Apply suggestions from flake8-implicit-str-concat

* Add changelog entry

* Add flake8 extensions in tox.ini

* Add flake8-mutable

* Update changelog entry

* Add `flake8-simplify` to linters (#1558)

* Add flake8-simplify

* Update flake8 excluded error codes & files

SIM114 involves recommending using a logical or, which can be confusing to
implement for newcomers...and also confusing to implement for me.

* Update type hints

* Remove .keys()

* Remove .keys()

* Remove .keys()

* Use contextlib.suppress instead of try/except/pass

* Simplify function

* Update type hints

* Simplify conditional

* Update flake8-simplify exclude rules

* Simplify conditional

* Simplify conditional

* Simplify conditionals

* Use numbers.Real instead of different specific types

* Add changelog entry

* Adding test cases for null point classification (#1554)

* Added test case for manual vector values.

* Added changelog entry

* Added test for multiple nullpoints

* Improved coverage

* Improved coverage

* Improved coverage

* Removed checking on surfaces, possibly unnecessary

* Splitted equality and testing atol

* Seperated null point find

* Added changelog entry

* Fixed doc error

* Edited changelog/doc

* Fixed docstring error

* Update changelog/1477.trivial.rst

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Added typing hint

* Added null point classifier

* Added changelog entry

* Added notebook

* Added notebook

* Fixed errors

* Fixed test

* Changed equality tolerance

* Fixed test case

* Update docs/notebooks/analysis/nullpoint.ipynb

Co-authored-by: Nick Murphy <[email protected]>

* Fixed name of uniform null point finder

* Update docs/bibliography.bib

Co-authored-by: Nick Murphy <[email protected]>

* Update changelog/1496.feature.rst

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Update plasmapy/analysis/nullpoint.py

Co-authored-by: Nick Murphy <[email protected]>

* Code review suggestions

* Update docs/notebooks/analysis/nullpoint.ipynb

Co-authored-by: Nick Murphy <[email protected]>

* Update docs/notebooks/analysis/nullpoint.ipynb

Co-authored-by: Nick Murphy <[email protected]>

* Update docs/notebooks/analysis/nullpoint.ipynb

Co-authored-by: Nick Murphy <[email protected]…