# Outline of PlasmaPy workshop

## Introduction

* Code of Conduct
* Why open science?
* Goals of PlasmaPy
- Open source software ecosystem for plasma research and education
* PlasmaPy in context
- Astropy
- Python in Heliophysics Community (SunPy, SpacePy, PySPEDAS, pysat)
* PlasmaPy website
* PlasmaPy documentation
- Contributor guide
* PlasmaPy
* Plasma Hack Week
* Terminology
- Subpackage vs. module

## Using PlasmaPy

* `astropy.units`
- Creating a `Quantity`
- Unit operations
- Unit conversions
- Detaching units from values
- Equivalencies
- eV ↔ K with `u.temperature_energy()`
- `astropy.constants`
- Units in PlasmaPy
- Optimizing unit operations
- `PhysicalType` objects
- PlasmaPy convention: code within PlasmaPy should use SI units
* `plasmapy.particles`
- Getting particle properties
- `Particle` objects
- `CustomParticle` objects and `molecule`
- `ParticleList` objects
- `DimensionlessParticle` objects
- Nuclear reactions
* `plasmapy.formulary`
- How the subpackage is structured
* `plasmapy.dispersion`
- Plasma dispersion function
- Two-fluid dispesion solvers
* `plasmapy.analysis`
* `plasmapy.diagnostics`
- Langmuir
- Charged particle radiography
* `plasmapy.simulation`
- Particle pusher
* Lite-functions
* Aliases

## `git` and GitHub

* Software carpentry lesson
* Using GitHub

## Getting set up to contribute (command line approach)

* Installing Python
*
* Cloning your fork of PlasmaPy's repository
* Setting up remotes
- Differences between `upstream` and `origin`
* Installing PlasmaPy for development (`pip install -e .`)
* Installing `pre-commit`

## Code contribution workflow

* `git fetch --all`
* `git checkout -b new-branch-name upstream/main`
* `git push --set-upstream origin new-branch-name`
* Cycle
- Edit file(s)
- `git commit -m "Edit file"`
- Best practices for a commit message
- `git push`
* Creating a pull request on GitHub
-
* Pulling changes from `upstream/main`
- `git fetch --all`
- `git pull upstream main`
* Edit file(s)
* `git add file.py`
* `git commit -m "Edited file..."`
* Best practices
- Writing a commit message
- Describing changes in a pull request

## Anatomy of a PlasmaPy function

* Function definition
* Docstring
* Tests
* Decorators
- `particle_input`
- `validate_quantities`
* Type hint annotations

## Testing PlasmaPy

* pytest
* `tox` (or `nox`?)
* Running PlasmaPy's tests
* Adding a test
* Testing exceptions and warnings
* Parametrizing tests
* Fixtures (?)
* Test-driven development
* GitHub Actions
* How to know which tests to write

## Linters and autoformatters

* Purpose
* `pre-commit`
* `black`
* `isort`
* `flake8` and its extensions
* `codespell`
* `nbqa`
* `pyupgrade`

## reStructuredText

* Inline markup (`*italic*` for *italic* and `**bold**` for **bold**)
- Bold & italic
- Backquotes for code samples
* Lists
* Title and section headers
* Links
* Roles
- `:math:`
- `:sup:` and `:sub:`
* Directives
- Code blocks (with pygments highlighting)
- Admonitions
* Tables
* Comments
* No nested inline markup 😿

## Documentation

* Building documentation locally
* Adding a docstring to a class or function
* numpydoc standard
* Writing narrative documentation in `docs/`
* Sphinx
* `docs/conf.py`
* `numpydoc` standard
* Bibliography and `:cite:`
* Glossary and `:term:`
* Adding a changelog entry
* `docs/conf.py`
* `docs/common_links.rst`
* `docs/api_static`
* Adding example notebooks

## Code review

* Code review mechanics on GitHub
* Best practices

## Additional stuff

* Lite-functions
- Numba and/or Cython
* Aliases

## Writing clean scientific software

* Variable names
* Extract function refactoring pattern
*