FEAT: add csv2fasta

[DriesSchaumont]

Description

FEAT: add csv2fasta

Issue ticket number

Closes #xxxx

Checklist before requesting a review

• I have performed a self-review of my code

• Conforms to the Contributing guidelines

• Proposed changes are described in the CHANGELOG.md

• I have tested my code with viash ns test --parallel -q <name or namespace>

• Check the correct box. Does this PR contain:

  • Breaking changes
  • New functionality
  • Major changes
  • Minor changes
  • Documentation
  • Bug fixes

[tverbeiren]

Comprehensive tests, very nice!

One of the tests is failing (as you probably have noticed yourself).

I wonder if we're going to run into issues with the --quote_character. CSV parsing libraries exist that auto-detect this and I wonder if we should do the same? The same holds for the delimiter, people often don't know what Excel will generate?

[DriesSchaumont]

Comprehensive tests, very nice!

One of the tests is failing (as you probably have noticed yourself).

I wonder if we're going to run into issues with the --quote_character. CSV parsing libraries exist that auto-detect this and I wonder if we should do the same? The same holds for the delimiter, people often don't know what Excel will generate?

I agree, here the python csv reader is used, which uses the 'excel' dialect by default, see https://docs.python.org/3/library/csv.html#csv.reader. Alternernatively, we could use a Sniffer to infer the dialect and use that: https://docs.python.org/3/library/csv.html#csv.Sniffer I would keep the 'quote_character' and 'delimiter' options, in order to override what the sniffer provided (with no override by default). Not really useful in automated pipelines, but worth including nonetheless WDYT?

[tverbeiren]

I would keep the 'quote_character' and 'delimiter' options, in order to override what the sniffer provided (with no override by default). Not really useful in automated pipelines, but worth including nonetheless WDYT?

Sure, good idea!

[rcannood]

@DriesSchaumont Is this PR ready to be merged?

[rcannood]

We decided to move this component to a separate package :)

[DriesSchaumont]

Closing in favour of viash-hub/craftbox#1