Interactive prompts for 'download' and 'launch'

[ErikDanielsson]

Added more interactive prompts to download and launch commands in accordance to #1009:

Download:

• Version selection list if -rflag is not set.
• Confirmation when --container (previously --singularity) and --singularity-cache flags are not set.
• Selection list of compression types when --compression flag is not set.
• Option to append export NXF_SINGULARITY_CACHEDIR=path to .bashrc if not already present.

Launch:

• Selection list to specify version of pipeline.

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[ewels]

ok @KevinMenden / others - I think that this is ready for final review + merge now. Let me know if you spot anything else 😁

[KevinMenden]

Great will go over it today :-)

[KevinMenden]

Code looks all good to me! Only a few small comments, mostly related to the singularity stuff. Didn't properly work for me while testing 🤔

[KevinMenden]

Unless we are planning to extend this choice list at some point, this could also just be flag instead of a prompt I think.
But also fine leaving it as a prompt.

[pontus]

My preference would be to leave it as a prompt. One could make a semi-reasonable case for offering download to pull e.g. docker images to the local instance.

[ewels]

Yeah, I went back on forth on this. At the moment it is just a --singularity flag. However, with the interactive prompts I would have needed to make it an on/off flag (--singularity --no-singularity). I don't love littering the cli with these, and figured that --container [str] was kind of more concise and had the added benefit of future-proofing.

@phue - as the only CharlieCloud user I know, does that have a similar concept of pulling image files? Would it ever be useful to add CharlieCloud image downloads to the nf-core download command for example?

[ewels]

And yes I also wondered about docker too @pontus 👍🏻

[KevinMenden]

As discussed on slack, I'll try to explain how the path autocompletion breaks for me.

When asked for a path, I start by typing the ~ symbol as a shortcut to my home directory. And from there I can then actually access directories that are in my home, and complete the path to the desired directory. So that the path in the prompt looks something like this:

~/path/to/cache_dir

Although when I then run it, it breaks and shows me that it used a path something like:

/home/kevin/path/to/cache_dir/~/path/to/cache_dir

Probably some weirdness with the os.abspath in combination with questionary.path.

[ewels]

Thanks for the brilliant reviewing both - this is picking up some really good edge case stuff! 😅 Keep it coming!

[KevinMenden]

Other than the weird home directory stuff, I couldn't find an issue 👍 good from my side!

[ewels]

@KevinMenden - I think that the weird home directory stuff should be fixed now, after the last commit. If you're still having strange behaviour with homedirs can you let me know?

[pontus]

I can't test right now, but it still seems there should be a return in the abort case (empty answer) as it's inside a while.

But I may be wrong and don't think that's super important, so merging is fine with me.

[ewels]

I think it should be fine as it's while cachedir_path is None: and it sets cachedir_path to False.. (If I'm looking at the code that you're talking about anyway)..

[pontus]

Ah, yes, should be fine.

[KevinMenden]

I double-checked again and now it works fine with ~ 👌

[ewels]

Thanks all!

[ewels]

Screencast demo:

nf-core-download.mov