Linting

[tkphd]

This PR addresses linting errors in the cookiecutter template, which are unfortunately propagated to every downstream project.

Tools used include:

• FlyCheck
• MarkdownLint
• YamlLint
• Flake8
• ShellCheck

[sierra-moxon]

Thanks @tkphd! This is great; can you confirm that you were able to test this by successfully creating a linkml project with the linted changes?

[tkphd]

Haha you want me to make sure the edited code works‽ Picky, picky!

... already found an error in list indentation, so, good call.

The file {{cookiecutter.project_name}}/project/prefixmap/{{cookiecutter.__project_slug}}.yaml fails linting, because it contains a Python dict (or JSON), not YAML as advertised. This was also noted in #22. This is out-of-scope for this PR, but I wonder what the appropriate "fix" is.

[tkphd]

OK, I have actually used the updated cookiecutter template, and can confirm that the generated files pass linting checks and make sense visually.

For fellow travelers, the command to use a specific branch is
cruft create --checkout <branch-or-tag-name> URL, so in this case I did

cruft create --checkout linting https://github.com/tkphd/linkml-project-cookiecutter