Added protein translation practice exercise

[golanor]

Here is a suggestion for the protein-translation exercise in Julia using string macros. Let me know what you think.

[cmcaine]

Hi, thanks for your interest. Please rebase and make the tests pass, then ping reviewers again.

[golanor]

Hi @cmcaine ,
There seems to be an issue with some versions of Julia when running this test. Do you suggest I change the test so that it would always pass, or should we try fixing the runner so there won't be a difference? It works for 1, and for the nightly (and 1.10 on my machine)

[cmcaine]

Julia 1.6 is the current LTS release, so I think we should still support it. The bug is probably because the macros are being expanded at different times on different releases, which might have been done deliberately or not.

We could fix that with eval (@test_throws TranslationError eval(:(@macroexpand rna"foo"))), but I think we should require the user to write a function that the string macro is then expected to call. I think this is usually the better option, and is definitely the better option in this case where it is very plausible that a user would want to find the translations of strings that are not known at compile time.

How does that sound to you?

[cmcaine]

as noted above

[golanor]

I made the changes, but then the string macro is a bit redundant, isn't it?

[cmcaine]

Suggested change

	codon_protein_dict = Dict(
	const codon_protein_dict = Dict(

[cmcaine]

Reordering these to encourage the student to work on the function first.

Also adding a link to the docs because macros are confusing.

Suggested change

	macro rna_str()
	# I'm a ribosome macro!
	end
	function rna_translator()
	# I'm a ribosome function!
	end
	function rna_translator()
	# I'm a ribosome function!
	end
	# Read the manual for more information on string macros:
	# https://docs.julialang.org/en/v1/manual/metaprogramming/#meta-non-standard-string-literals
	macro rna_str()
	# I'm a ribosome macro!
	end

[cmcaine]

The macro serves the same purpose as other string macros:

1. Mostly a convenient/pretty shorthand
2. Also a way to ensure a computation can happen at compile-time (good for e.g. Regex so that the moderately expensive PCRE regex compilation step can be done at the same time as the Julia compilation step).

What do you want the student to learn from the exercise?

I suggest changing all instances of rna"..." in the tests to rna_translator("...") and adding a couple of tests of the macro at the end.

Reason: the function interface is easier to test and understand for the student.

Alternatively, we could remove the macro version entirely.

[golanor]

I wanted to teach both macro writing and creating an exception. I'll settle for only learning how to create a new exception.

[cmcaine]

Function names should describe an action, not an object, according to the Julia style guide and general practice.

How about one of these names? Presented in my preference order.

Suggested change

	function rna_translator(rna::String)
	function rna_to_amino_acids(rna::String)

Suggested change

	function rna_translator(rna::String)
	function rna_to_protein(rna::String)

Suggested change

	function rna_translator(rna::String)
	function translate_rna(rna::String)

[cmcaine]

Feel free to put the string macro back in as a bonus question, if you like. The rot13 practice exercise has an example of this.

[golanor]

Renamed and added the macro as a bonus question

[golanor]

Can we merge this?

[cmcaine]

Sorry, I missed the updates. I'll try to take a look this week. Please ping me again if I don't.

[cmcaine]

Note to self. Last two commiys look good. Like the rename. Recheck the diff with master before merge.

[golanor]

ping @cmcaine

[golanor]

@cmcaine Can we merge?

[cmcaine]

Thanks for the reminder.

What do you think of these suggestions?

[golanor]

I comitted the suggested changes

[cmcaine]

Cool. The example.jl will need to be changed to throw Argument error.