Adapt ESMValTool to new configuration

[schlunma]

Description

This PR adapt all parts of ESMValTool to the new configuration (see ESMValGroup/ESMValCore#2448).

• Related to New configuration file plan ESMValCore#2371
• Fixes Documentation build is broken #3762

Deprecation

Similar to the corresponding ESMValCore PR, this PR deprecates the command line option --config_file for esmvaltool data format/download/prepare. This option is scheduled for removal in version 2.14.0. Please use the option config_dir instead.

Example:

Old syntax:

esmvaltool data format --config_file=~/my/config/file.yml WOA

New syntax:

esmvaltool data format --config_dir=~/my/config/ WOA

See ESMValGroup/ESMValCore#2448 and ESMValGroup/ESMValCore#2371 for further details.

---

Before you get started

• ☝ Create an issue to discuss what you are going to do

Checklist

It is the responsibility of the author to make sure the pull request is ready to review. The icons indicate whether the item will be subject to the 🛠 Technical or 🧪 Scientific review.

• 🛠 This pull request has a descriptive title
• 🛠 Code is written according to the code quality guidelines
• 🛠 Documentation is available
• 🛠 Tests run successfully
• 🛠 The list of authors is up to date
• 🛠 Any changed dependencies have been added or removed correctly
• 🛠 All checks below this pull request were successful

---

To help with the number of pull requests:

• 🙏 We kindly ask you to review two other open pull requests in this repository

[bouweandela]

Use double backticks around rootpath to make it monospace (a single backtick is italic and the convention is to use monospace for things that have to be typed exactly like that)

[schlunma]

Yeah, I am always unsure about this. Numpy recommends to enclose parameter names in single backticks, and they seem to be aware of the different meanings of single backticks in markdown and reST. I've also seen the usage of italic font for parameters in Numpy's (and other project's) API documentation (e.g., bins here). That's why I used single backticks here.

However, I can totally see your point about the double backticks. As long as we use one convention consistently (and we're currently certainly not doing that), I guess both are fine? So maybe we should just once and for all decide on one and continue to use that?

[schlunma]

Changed in ce62d9f and 75e2b33

[bouweandela]

Thanks! I assumed our convention was to use monospace font for things that need to be written exactly like that to work and all the other cases were people who just forgot that in .rst you need double backticks to create monospace fonts. Maybe we need to write this in our contributor docs somewhere too. From the text you linked it looks like numpy plans to adopt the same convention, but are working on some feature to make that work with single backticks:

This guide continues to recommended that parameter names be enclosed within single backticks. Currently, this may cause parameter names to render improperly and cause warnings, but numpydoc will soon release a feature that causes them to render as monospaced hyperlinks to the parameter documentation.

[bouweandela]

Nice work! Just a few comments on improving the formatting and possibly removing some unnecessary code from the recipe filler.

[bouweandela]

Thanks for making all the changes @schlunma! I believe there is one comment still outstanding: #3761 (comment), could you have a look?

[schlunma]

Thanks for making all the changes @schlunma! I believe there is one comment still outstanding: #3761 (comment), could you have a look?

Done in f0e7565