Add apply CLI

[kadarakos]

New spacy cli command to make annotating new documents with the a trained pipeline convenient by just running a single command.

Description

Adds a new spacy cli command called apply that takes a model and a file or directory as input.
The file or the files in the directory should be of the following formats:

1. .spacy file.
2. .jsonl file where the provided --text-key is used to find the documents.
3. Any other file found is considered a plain text file containing a single document.

Given the input file or directory apply generates a .spacy file containing the Doc objects produced by the model.

Types of change

New feature

Checklist

• I confirm that I have the right to submit this contribution under the project's MIT license.
• I ran the tests, and all new and existing tests passed.
• My changes don't require a change to the documentation, or if they do, I've added all required information.

[kadarakos]

The way the data loading is done is with a bunch of nested try/except blocks, which I feel like is something we would like to avoid in general but it felt valid here.

Also this cli command is really short and simple compared to the rest so I feel like I must have missed a lot of things.

[adrianeboyd]

I think it would make more sense to go by file ending here (maybe .spacy vs. not-.spacy) and take it from there?

[kadarakos]

I think it would make more sense to go by file ending here (maybe .spacy vs. not-.spacy) and take it from there?

okok and then only the decode error remains in the tryexcept

[svlandeg]

It looks like this PR should be good to merge as soon as the documentation is added?

[polm]

Thanks for working on this, I think it's a really important feature to have! I'm sorry I didn't look at it early.

I have comments and docs fixes, but they're mostly pretty minor formatting stuff.

[svlandeg]

Thanks again for all your work on this Akos, this will be a great new command to have!