[JOSS] Grammar adjustments and typo fixes, add software package citations

[Zeitsperre]

Changes

• Fixed a few phrases for small typos, whitespace, and grammar.
• Added the citations for a few pieces of software mentioned.

General Comments

• There are a few places where Jupyter notebooks are directly linked to in the body of the text. This can cause problems down-the-line if you wish/need to change the name of a notebook. I would suggest to point to the documentation or to the Zenodo entry for the notebook in question in case that URL needs to change.

Ref: openjournals/joss-reviews#5525

[crvernon]

One minor edit mentioned in-text.